d04d32c645edb005fc4811ea1f4e70de6c1c43a5
hiram
  Tue Jul 30 17:05:54 2019 -0700
fixup directory name clash for bedJoinTabOffset refs #23806

diff --git src/userApps/fetchKentSource.sh src/userApps/fetchKentSource.sh
index 6f1f297..6727a92 100755
--- src/userApps/fetchKentSource.sh
+++ src/userApps/fetchKentSource.sh
@@ -1,300 +1,303 @@
 #!/bin/bash
 #
 # exit on any error:
 set -beEu -o pipefail
 
 # switching to beta for version 286
 export branch="beta"
 
 # to use the top of the source tree, uncomment this branch=HEAD statment
 # and comment out the one above.  This is sometimes useful when there
 # are new fixes in the source tree in between beta releases.
 # Note, the top of the source tree could be broken at any time, it is on
 # a 10-minute update cycle with live work taking place.
 
 # export branch="HEAD"
 
 # These selective git archive commands only work up to a certain size
 # of fetched source (number of arguments), hence the multiple set of
 # individual fetches to get all the parts
 
 rm -f part1Src.zip part2Src.zip part3Src.zip part4Src.zip part5Src.zip
 export partNumber=1
 export ofN="of 5"
 
 # this util changed from being in a directory to being a script
 # the extract can't overwrite the directory with a file
 rm -fr kent/src/utils/uniprotLift
+# v385 this util changed from a script by this name to a directory
+# and the script changed to a .py name
+rm -fr kent/src/utils/bedJoinTabOffset
 
 echo "fetch kent source part ${partNumber} ${ofN}" 1>&2
 git archive --format=zip -9 --remote=git://genome-source.soe.ucsc.edu/kent.git \
 --prefix=kent/ ${branch} \
 src/machTest.sh \
 src/checkUmask.sh \
 src/ameme \
 src/aladdin \
 src/blat \
 src/dnaDust \
 src/fuse \
 src/gfClient \
 src/gfServer \
 src/index \
 src/makefile \
 src/meta \
 src/parasol \
 src/primeMate \
 src/product \
 src/protDust \
 src/weblet \
 src/inc \
 src/utils \
 src/jkOwnLib \
 src/lib \
 src/hg/affyTransciptome \
 src/hg/agpAllToFaFile \
 src/hg/agpCloneCheck \
 src/hg/agpCloneList \
 src/hg/agpToFa \
 src/hg/agpToGl \
 src/hg/altSplice \
 src/hg/autoDtd \
 src/hg/autoSql \
 src/hg/autoXml \
 src/hg/bedIntersect \
 src/hg/bedItemOverlapCount \
 src/hg/bedOrBlocks \
 src/hg/bedSort \
 src/hg/bedSplitOnChrom \
 src/hg/bedToGenePred \
 src/hg/blastToPsl \
 src/hg/borfBig \
 src/hg/checkCoverageGaps \
 src/hg/checkHgFindSpec \
 src/hg/checkTableCoords \
 src/hg/ctgFaToFa \
 src/hg/ctgToChromFa \
 src/hg/dbTrash \
 src/hg/embossToPsl \
 src/hg/estOrient \
 src/hg/encode/validateFiles \
 src/hg/fakeFinContigs \
 src/hg/fakeOut \
 src/hg/featureBits \
 src/hg/ffaToFa \
 src/hg/fishClones \
 src/hg/fqToQa \
 src/hg/fqToQac \
 src/hg/fragPart \
 src/hg/gbGetEntries \
 src/hg/gbOneAcc > part${partNumber}Src.zip
 
 unzip -o -q part${partNumber}Src.zip
 
 ((partNumber++))
 echo "fetch kent source part ${partNumber} ${ofN}" 1>&2
 
 git archive --format=zip -9 --remote=git://genome-source.soe.ucsc.edu/kent.git \
 --prefix=kent/ ${branch} \
 src/hg/gbToFaRa \
 src/hg/geneBounds \
 src/hg/genePredHisto \
 src/hg/genePredSingleCover \
 src/hg/genePredToBed \
 src/hg/genePredToFakePsl \
 src/hg/genePredToGtf \
 src/hg/genePredToMafFrames \
 src/hg/getFeatDna \
 src/hg/getRna \
 src/hg/getRnaPred \
 src/hg/gpStats \
 src/hg/gpToGtf \
 src/hg/gpcrParser \
 src/hg/gsBig \
 src/hg/hgChroms \
 src/hg/hgGetAnn \
 src/hg/hgKnownGeneList \
 src/hg/hgSelect \
 src/hg/hgSpeciesRna \
 src/hg/hgTablesTest \
 src/hg/hgsql \
 src/hg/hgsqlSwapTables \
 src/hg/hgsqlTableDate \
 src/hg/hgsqladmin \
 src/hg/hgsqldump \
 src/hg/hgsqlimport \
 src/hg/inc \
 src/hg/intronEnds \
 src/hg/lib \
 src/hg/lfsOverlap \
 src/hg/liftAcross \
 src/hg/liftAgp \
 src/hg/liftFrags \
 src/hg/liftUp \
 src/hg/liftOver \
 src/hg/makefile \
 src/hg/makeDb/hgLoadWiggle \
 src/hg/makeDb/hgGcPercent \
 src/hg/utils \
 src/hg/maskOutFa \
 src/hg/mdToNcbiLift \
 src/hg/mrnaToGene \
 src/hg/orthoMap \
 src/hg/patCount \
 src/hg/perf \
 src/hg/pslCat \
 src/hg/pslCheck \
 src/hg/pslCoverage \
 src/hg/pslCDnaFilter \
 src/hg/pslPretty \
 src/hg/pslReps \
 src/hg/pslSort \
 src/hg/pslSomeRecords \
 src/hg/pslDropOverlap > part${partNumber}Src.zip
 
 unzip -o -q part${partNumber}Src.zip
 
 ((partNumber++))
 echo "fetch kent source part ${partNumber} ${ofN}" 1>&2
 
 git archive --format=zip -9 --remote=git://genome-source.soe.ucsc.edu/kent.git \
 --prefix=kent/ ${branch} \
 src/hg/pslFilter \
 src/hg/pslFilterPrimers \
 src/hg/pslGlue \
 src/hg/pslHisto \
 src/hg/pslHitPercent \
 src/hg/pslIntronsOnly \
 src/hg/pslPairs \
 src/hg/pslPartition \
 src/hg/pslQuickFilter \
 src/hg/pslRecalcMatch \
 src/hg/pslSelect \
 src/hg/pslSimp \
 src/hg/pslSortAcc \
 src/hg/pslSplitOnTarget \
 src/hg/pslStats \
 src/hg/pslSwap \
 src/hg/pslToBed \
 src/hg/pslUnpile \
 src/hg/pslxToFa \
 src/hg/qa \
 src/hg/qaToQac \
 src/hg/qacAgpLift \
 src/hg/qacToQa \
 src/hg/qacToWig \
 src/hg/recycleDb \
 src/hg/relPairs \
 src/hg/reviewSanity \
 src/hg/rnaStructure \
 src/hg/scanRa \
 src/hg/semiNorm \
 src/hg/sim4big \
 src/hg/snp \
 src/hg/snpException \
 src/hg/spideyToPsl \
 src/hg/encode3 \
 src/hg/splitFa \
 src/hg/splitFaIntoContigs \
 src/hg/sqlEnvTest.sh \
 src/hg/sqlToXml \
 src/hg/test \
 src/hg/trfBig \
 src/hg/txCds \
 src/hg/txGene \
 src/hg/txGraph \
 src/hg/uniqSize \
 src/hg/updateStsInfo \
 src/hg/xmlCat \
 src/hg/xmlToSql \
 src/hg/hgTables \
 src/hg/near \
 src/hg/pslDiff \
 src/hg/sage \
 src/hg/gigAssembler/checkAgpAndFa \
 src/hg/genePredCheck > part${partNumber}Src.zip
 
 unzip -o -q part${partNumber}Src.zip
 
 ((partNumber++))
 echo "fetch kent source part ${partNumber} ${ofN}" 1>&2
 
 git archive --format=zip -9 --remote=git://genome-source.soe.ucsc.edu/kent.git \
 --prefix=kent/ ${branch} \
 src/hg/makeDb/makefile \
 src/hg/makeDb/hgAar \
 src/hg/makeDb/hgAddLiftOverChain \
 src/hg/makeDb/hgBbiDbLink \
 src/hg/makeDb/hgClonePos \
 src/hg/makeDb/hgCountAlign \
 src/hg/makeDb/hgCtgPos \
 src/hg/makeDb/hgDeleteChrom \
 src/hg/makeDb/hgExperiment \
 src/hg/makeDb/hgExtFileCheck \
 src/hg/makeDb/hgFakeAgp \
 src/hg/makeDb/hgFindSpec \
 src/hg/makeDb/hgGeneBands \
 src/hg/makeDb/hgGenericMicroarray \
 src/hg/makeDb/hgPar \
 src/hg/makeDb/hgGoldGapGl \
 src/hg/makeDb/hgKgGetText \
 src/hg/makeDb/hgKgMrna \
 src/hg/makeDb/hgKnownMore \
 src/hg/makeDb/hgKnownMore.oo21 \
 src/hg/makeDb/hgLoadBed \
 src/hg/makeDb/hgLoadBlastTab \
 src/hg/makeDb/hgLoadChain \
 src/hg/makeDb/hgLoadChromGraph \
 src/hg/makeDb/hgLoadGenePred \
 src/hg/makeDb/hgLoadItemAttr \
 src/hg/makeDb/hgLoadMaf \
 src/hg/makeDb/hgLoadMafFrames \
 src/hg/makeDb/hgLoadNet \
 src/hg/makeDb/hgLoadOut \
 src/hg/makeDb/hgLoadOutJoined \
 src/hg/makeDb/hgLoadPsl \
 src/hg/makeDb/hgLoadSeq \
 src/hg/makeDb/hgLoadSample \
 src/hg/makeDb/hgLoadSqlTab \
 src/hg/makeDb/hgMapMicroarray \
 src/hg/makeDb/hgMedianMicroarray \
 src/hg/makeDb/hgNibSeq \
 src/hg/makeDb/hgPepPred \
 src/hg/makeDb/hgRatioMicroarray \
 src/hg/makeDb/hgDropSplitTable \
 src/hg/makeDb/hgRenameSplitTable \
 src/hg/makeDb/hgSanger20 \
 src/hg/makeDb/hgSanger22 \
 src/hg/makeDb/hgStanfordMicroarray \
 src/hg/makeDb/hgStsAlias \
 src/hg/makeDb/hgStsMarkers \
 src/hg/makeDb/hgTomRough \
 src/hg/makeDb/hgTpf \
 src/hg/makeDb/hgTraceInfo \
 src/hg/makeDb/hgTrackDb \
 src/hg/makeDb/hgWaba \
 src/hg/makeDb/ldHgGene \
 src/hg/makeDb/hgMrnaRefseq \
 src/hg/makeDb/schema \
 src/hg/makeDb/tfbsConsLoc \
 src/hg/makeDb/tfbsConsSort > part${partNumber}Src.zip
 
 unzip -o -q part${partNumber}Src.zip
 
 ((partNumber++))
 echo "fetch kent source part ${partNumber} ${ofN}" 1>&2
 
 git archive --format=zip -9 --remote=git://genome-source.soe.ucsc.edu/kent.git \
 --prefix=kent/ ${branch} \
 src/parasol \
 src/htslib \
 src/hg/pslToChain \
 src/hg/makeDb/outside \
 src/hg/makeDb/trackDbRaFormat \
 src/hg/makeDb/trackDbPatch \
 src/hg/mouseStuff \
 src/hg/ratStuff \
 src/hg/nci60 \
 src/hg/visiGene/knownToVisiGene \
 src/hg/visiGene/hgVisiGene > part${partNumber}Src.zip
 
 unzip -o -q part${partNumber}Src.zip